1. Quick start

The easiest way to install Bactabolize is via a conda environment. You can install conda as descrbed here. We recommend mamba for installing Bactabolize, due to speed.

# Install mamba in base conda
conda install -n base -y -c conda-forge mamba

# Create and activate environment via mamba
mamba create -n bactabolize -y -c kelwyres -c bioconda -c conda-forge 'bactabolize==1.0.4'
conda activate bactabolize

# Test installation
bactabolize -h

# Create draft model
bactabolize draft_model \
    --assembly_fp input_assembly.fasta \
    --ref_genes_fp reference_model_genes.ffn \
    --ref_proteins_fp reference_model_genes.faa \
    --ref_model_fp reference_model.json \
    --biomass_reaction_id YOUR_BIOMASS_ID \
    --media_type m9 \
    --atmosphere_type aerobic \
    --min_coverage 25 \
    --min_pident 80 \
    --output_fp input_assembly

# Run simulated nutrient growth profiles (FBA)
bactabolize fba \
    --model_fp input_assembly_model.json \
    --fba_spec_name m9 \
    --output_fp input_assembly_model_FBA.tsv \
    --fba_open_value -20

# Run single gene knockout analysis (SGK)
bactabolize sgk \
  --model_fp input_assembly_model.json \
  --media_type m9 \
  --atmosphere_type aerobic \
  --output_fp input_assembly_model_sgk_m9_O2.tsv

Test data is also included in the data/test_data directory, along with expected outputs from commands.